Software for analysing ion mobility mass spectrometry data to improve peptide identification

• Published in: Proteomics (Weinheim) Vol. 12; no. 12; pp. 1912 - 1916
• Main Authors: Xia, Dong, Ghali, Fawaz, Gaskell, Simon J., O'Cualain, Ronan, Sims, Paul F. G., Jones, Andrew R.
• Format: Journal Article
• Language: English
• Published: Weinheim Blackwell Publishing Ltd 01-06-2012; Wiley-VCH; Wiley Subscription Services, Inc
• Subjects: Amino Acid Sequence; Analytical, structural and metabolic biochemistry; Bioinformatics; Biological and medical sciences; Computational Biology - methods; Database search; Databases, Protein; Fundamental and applied biological sciences. Psychology; Humans; Ion mobility; Linear Models; Mass Spectrometry - methods; Miscellaneous; Molecular Sequence Data; Peptide fragmentation; Peptide identification; Peptides; Peptides - analysis; Peptides - chemistry; Proteins; Proteomics; Software; Peptide fragmentation; Peptide identification; Peptides; Ion mobility; Proteomics; Database; Ion spectrometry; Identification; Software; Database search; Mass spectrometry; Bioinformatics
• ISSN: 1615-9853; 1615-9861
• DOI: 10.1002/pmic.201200029

The development of ion mobility (IM) MS instruments has the capability to provide an added dimension to peptide analysis pipelines in proteomics, but, as yet, there are few software tools available for analysing such data. IM can be used to provide additional separation of parent ions or product ions following fragmentation. In this work, we have created a set of software tools that are capable of converting three dimensional IM data generated from analysis of fragment ions into a variety of formats used in proteomics. We demonstrate that IM can be used to calculate the charge state of a fragment ion, demonstrating the potential to improve peptide identification by excluding non‐informative ions from a database search. We also provide preliminary evidence of structural differences between b and y ions for certain peptide sequences but not others. All software tools and data sets are made available in the public domain at http://code.google.com/p/ion-mobility-ms-tools/.